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Hi Reza,<br>
<br>
geometry of refined model may be severely distorted if your target
map on a wrong scale (magnification).<br>
<br>
Some relevant reading:<br>
<br>
1)
<br>
Automatic estimation and correction of anisotropic
magnification,distortion in electron microscopes,Timothy Grant,
Nikolaus Grigorieff
<br>
Journal of Structural Biology 192 (2015) 204–208
<br>
<br>
2)
<br>
Electron cryomicroscopy observation of rotational states in a
eukaryotic V-ATPase,
<br>
Jianhua Zhao, Samir Benlekbir & John L. Rubinstein
<br>
Nature 521, 241–245 (14 May 2015)
<br>
<br>
3)
<br>
Description and comparison of algorithms for correcting anisotropic
magnification in cryo-EM images.
<br>
Jianhua Zhao, Marcus A. Brubaker, Samir Benlekbir, John L.
Rubinstein
<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 2/8/16 02:38, Reza Khayat wrote:<br>
</div>
<blockquote cite="mid:1454927907175.40953@ccny.cuny.edu" type="cite">
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<p>Hi Oliver,<br>
</p>
<p><br>
</p>
<p>Out of curiosity:</p>
<p> 1. what kind of R-factors and CC-values do you get when
refining against the two different pixel size? <br>
</p>
<p> 2. how different are your refined pixel sizes from one
reconstruction to another?<br>
</p>
<p> 3. how much of an affect does the wrong pixel size have on
your downstream structure analysis (e.g. BDA, ASA,
electrostatic...)? </p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
<br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper"
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:; margin:0">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
color="#000000" face="Calibri, sans-serif"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb-bounces@phenix-online.org"><phenixbb-bounces@phenix-online.org></a> on behalf of
Oliver Clarke <a class="moz-txt-link-rfc2396E" href="mailto:olibclarke@gmail.com"><olibclarke@gmail.com></a><br>
<b>Sent:</b> Monday, February 8, 2016 4:28 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] Refine pixel size of map (for EM
data)?</font>
<div> </div>
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<div>
<div dir="ltr">
<div>
<div>Hello,<br>
<br>
</div>
I wonder whether it would be possible to add an option for
phenix.real_space_refine to allow refinement of the pixel
size of the map (or the unit cell dimensions - just an
overall size scale factor), and write out the altered map
at the end of refinement.<br>
<br>
Although we try to calibrate this as best as we are able
at the time of data collection, it is never perfect - for
example, in one case I have dealt with, our nominal pixel
size out of the scope is 1.19 Å, but the pixel size
calibrated based on a crystal structure of a fragment of
the protein is 1.25 Å. This is not a huge difference, but
it is sufficient I think to have a substantial impact on
refinement, particularly as regards clash assessment and
H-bond/sec struc restraints.
<br>
<br>
In cases where one does not have a solved crystal
structure to use for calibration, perhaps refining the
pixel size in conjunction with the geometry might be of
some use?<br>
<br>
</div>
<div>Cheers,<br>
</div>
<div>Oli<br>
</div>
</div>
</div>
</div>
<br>
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